Starting phenix.real_space_refine on Mon Mar 11 01:07:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/03_2024/7ddp_30653.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/03_2024/7ddp_30653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/03_2024/7ddp_30653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/03_2024/7ddp_30653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/03_2024/7ddp_30653.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/03_2024/7ddp_30653.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4143 2.51 5 N 1065 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6477 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "C" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1529 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.44, per 1000 atoms: 1.15 Number of scatterers: 6477 At special positions: 0 Unit cell: (102.356, 97.3875, 105.338, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1231 8.00 N 1065 7.00 C 4143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 53 " " NAG C 601 " - " ASN C 343 " Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 56.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.030A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.596A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.529A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.806A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.205A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 219 through 252 removed outlier: 4.122A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.775A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.623A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.708A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 414 removed outlier: 3.557A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 532 removed outlier: 4.283A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.098A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.726A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.335A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.680A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.784A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.523A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.328A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.540A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 310 hydrogen bonds defined for protein. 881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2071 1.35 - 1.46: 1708 1.46 - 1.58: 2820 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6657 Sorted by residual: bond pdb=" N TYR C 489 " pdb=" CA TYR C 489 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.21e-02 6.83e+03 9.23e+00 bond pdb=" N PHE C 456 " pdb=" CA PHE C 456 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.41e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 ... (remaining 6652 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 212 106.67 - 113.50: 3507 113.50 - 120.33: 2542 120.33 - 127.16: 2694 127.16 - 133.99: 95 Bond angle restraints: 9050 Sorted by residual: angle pdb=" N VAL A 318 " pdb=" CA VAL A 318 " pdb=" C VAL A 318 " ideal model delta sigma weight residual 112.80 109.72 3.08 1.15e+00 7.56e-01 7.19e+00 angle pdb=" C LEU A 144 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 120.44 123.89 -3.45 1.30e+00 5.92e-01 7.05e+00 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.38 111.77 -3.39 1.35e+00 5.49e-01 6.29e+00 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 119.69 -5.29 2.30e+00 1.89e-01 5.28e+00 angle pdb=" N ILE A 421 " pdb=" CA ILE A 421 " pdb=" C ILE A 421 " ideal model delta sigma weight residual 112.98 110.18 2.80 1.25e+00 6.40e-01 5.03e+00 ... (remaining 9045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3599 17.97 - 35.94: 318 35.94 - 53.91: 53 53.91 - 71.88: 12 71.88 - 89.85: 11 Dihedral angle restraints: 3993 sinusoidal: 1671 harmonic: 2322 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 8.59 84.41 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 15.94 77.06 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 23.03 69.97 1 1.00e+01 1.00e-02 6.31e+01 ... (remaining 3990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 578 0.029 - 0.058: 260 0.058 - 0.087: 72 0.087 - 0.115: 51 0.115 - 0.144: 4 Chirality restraints: 965 Sorted by residual: chirality pdb=" CA PHE C 456 " pdb=" N PHE C 456 " pdb=" C PHE C 456 " pdb=" CB PHE C 456 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE A 468 " pdb=" N ILE A 468 " pdb=" C ILE A 468 " pdb=" CB ILE A 468 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA PRO A 253 " pdb=" N PRO A 253 " pdb=" C PRO A 253 " pdb=" CB PRO A 253 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 962 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 488 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C CYS C 488 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS C 488 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR C 489 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 500 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 583 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.020 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 103 2.66 - 3.22: 6014 3.22 - 3.78: 10236 3.78 - 4.34: 14322 4.34 - 4.90: 23151 Nonbonded interactions: 53826 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.100 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.176 2.440 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.236 2.440 nonbonded pdb=" O SER A 254 " pdb=" OG SER A 254 " model vdw 2.241 2.440 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.302 2.520 ... (remaining 53821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.200 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.800 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6657 Z= 0.186 Angle : 0.555 7.087 9050 Z= 0.310 Chirality : 0.040 0.144 965 Planarity : 0.003 0.036 1165 Dihedral : 14.105 89.849 2484 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.29 % Allowed : 2.73 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.27), residues: 788 helix: -0.20 (0.24), residues: 395 sheet: -2.05 (0.62), residues: 56 loop : -1.70 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 302 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.001 PHE A 369 TYR 0.015 0.001 TYR A 381 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7258 (pttt) REVERT: A 195 HIS cc_start: 0.8245 (m90) cc_final: 0.8040 (m170) REVERT: A 202 TYR cc_start: 0.7367 (t80) cc_final: 0.7158 (t80) REVERT: A 474 MET cc_start: 0.7289 (mmp) cc_final: 0.6871 (mmt) outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.1966 time to fit residues: 32.9332 Evaluate side-chains 98 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 489 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6657 Z= 0.268 Angle : 0.586 7.022 9050 Z= 0.297 Chirality : 0.043 0.153 965 Planarity : 0.004 0.031 1165 Dihedral : 5.502 55.526 967 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.87 % Allowed : 11.37 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.28), residues: 788 helix: 0.64 (0.25), residues: 402 sheet: -1.72 (0.60), residues: 60 loop : -1.23 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 302 HIS 0.004 0.001 HIS A 378 PHE 0.019 0.002 PHE A 369 TYR 0.029 0.002 TYR A 381 ARG 0.003 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8070 (mmmm) cc_final: 0.7314 (pttt) REVERT: A 474 MET cc_start: 0.7346 (mmp) cc_final: 0.6790 (mmp) REVERT: C 378 LYS cc_start: 0.6593 (mtpt) cc_final: 0.5948 (ptmm) REVERT: C 492 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6837 (mp) outliers start: 13 outliers final: 5 residues processed: 107 average time/residue: 0.1894 time to fit residues: 27.0416 Evaluate side-chains 95 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 0.0770 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6657 Z= 0.141 Angle : 0.505 6.893 9050 Z= 0.254 Chirality : 0.040 0.134 965 Planarity : 0.003 0.027 1165 Dihedral : 4.764 53.135 967 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.87 % Allowed : 13.09 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.29), residues: 788 helix: 1.25 (0.26), residues: 402 sheet: -1.60 (0.63), residues: 58 loop : -0.83 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.015 0.001 PHE A 369 TYR 0.009 0.001 TYR A 381 ARG 0.001 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7969 (mmmm) cc_final: 0.7264 (pttt) REVERT: A 474 MET cc_start: 0.7307 (mmp) cc_final: 0.6709 (mmp) REVERT: C 378 LYS cc_start: 0.6545 (mtpt) cc_final: 0.6173 (ptmm) REVERT: C 452 LEU cc_start: 0.7827 (mp) cc_final: 0.7583 (mm) outliers start: 13 outliers final: 12 residues processed: 112 average time/residue: 0.1925 time to fit residues: 29.2215 Evaluate side-chains 111 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6657 Z= 0.161 Angle : 0.519 8.258 9050 Z= 0.260 Chirality : 0.040 0.133 965 Planarity : 0.003 0.026 1165 Dihedral : 4.652 49.981 967 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.16 % Allowed : 14.96 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.30), residues: 788 helix: 1.47 (0.26), residues: 401 sheet: -1.59 (0.65), residues: 58 loop : -0.67 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.001 PHE A 369 TYR 0.013 0.001 TYR A 381 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7279 (pttt) REVERT: A 474 MET cc_start: 0.7411 (mmp) cc_final: 0.6776 (mmp) REVERT: C 378 LYS cc_start: 0.6501 (mtpt) cc_final: 0.6142 (ptmm) REVERT: C 409 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: C 452 LEU cc_start: 0.7866 (mp) cc_final: 0.7626 (mm) outliers start: 15 outliers final: 10 residues processed: 115 average time/residue: 0.1801 time to fit residues: 28.0443 Evaluate side-chains 111 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.0050 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6657 Z= 0.154 Angle : 0.512 9.310 9050 Z= 0.256 Chirality : 0.040 0.130 965 Planarity : 0.003 0.026 1165 Dihedral : 4.499 45.883 967 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.30 % Allowed : 15.11 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 788 helix: 1.56 (0.26), residues: 402 sheet: -1.64 (0.66), residues: 60 loop : -0.55 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.001 PHE A 369 TYR 0.012 0.001 TYR A 381 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8015 (mmmm) cc_final: 0.7259 (pttt) REVERT: A 474 MET cc_start: 0.7494 (mmp) cc_final: 0.7264 (mmt) REVERT: C 378 LYS cc_start: 0.6457 (mtpt) cc_final: 0.6221 (ptmm) REVERT: C 409 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: C 452 LEU cc_start: 0.7856 (mp) cc_final: 0.7624 (mm) outliers start: 16 outliers final: 14 residues processed: 110 average time/residue: 0.1801 time to fit residues: 26.7996 Evaluate side-chains 114 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6657 Z= 0.145 Angle : 0.501 9.383 9050 Z= 0.251 Chirality : 0.040 0.129 965 Planarity : 0.003 0.024 1165 Dihedral : 4.337 41.487 967 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.16 % Allowed : 15.97 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.30), residues: 788 helix: 1.63 (0.26), residues: 402 sheet: -1.51 (0.66), residues: 60 loop : -0.52 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.015 0.001 PHE A 369 TYR 0.011 0.001 TYR A 381 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7287 (pttt) REVERT: A 474 MET cc_start: 0.7464 (mmp) cc_final: 0.6753 (mmp) REVERT: C 409 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7208 (mp10) outliers start: 15 outliers final: 14 residues processed: 110 average time/residue: 0.2125 time to fit residues: 30.8689 Evaluate side-chains 114 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.4980 chunk 42 optimal weight: 0.1980 chunk 63 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6657 Z= 0.125 Angle : 0.484 9.415 9050 Z= 0.242 Chirality : 0.039 0.127 965 Planarity : 0.003 0.023 1165 Dihedral : 4.073 38.478 967 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.30 % Allowed : 15.83 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.30), residues: 788 helix: 1.78 (0.26), residues: 402 sheet: -1.35 (0.67), residues: 60 loop : -0.41 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.014 0.001 PHE A 369 TYR 0.009 0.001 TYR A 516 ARG 0.001 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7965 (mmmm) cc_final: 0.7258 (pttt) REVERT: A 474 MET cc_start: 0.7479 (mmp) cc_final: 0.7251 (mmt) REVERT: C 409 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: C 452 LEU cc_start: 0.7805 (mp) cc_final: 0.7551 (mm) outliers start: 16 outliers final: 14 residues processed: 110 average time/residue: 0.1847 time to fit residues: 27.3321 Evaluate side-chains 111 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6657 Z= 0.279 Angle : 0.596 9.492 9050 Z= 0.299 Chirality : 0.042 0.135 965 Planarity : 0.004 0.027 1165 Dihedral : 4.917 39.657 967 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.59 % Allowed : 16.26 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 788 helix: 1.30 (0.25), residues: 401 sheet: -1.44 (0.68), residues: 60 loop : -0.46 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 477 HIS 0.005 0.001 HIS A 373 PHE 0.016 0.002 PHE A 32 TYR 0.028 0.002 TYR A 381 ARG 0.003 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.615 Fit side-chains REVERT: A 114 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7301 (pttt) REVERT: C 378 LYS cc_start: 0.6620 (mtpt) cc_final: 0.5998 (ptmm) REVERT: C 409 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: C 488 CYS cc_start: 0.6195 (m) cc_final: 0.5993 (m) outliers start: 18 outliers final: 14 residues processed: 106 average time/residue: 0.1811 time to fit residues: 25.8419 Evaluate side-chains 109 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.0070 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.0020 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6657 Z= 0.132 Angle : 0.502 9.379 9050 Z= 0.252 Chirality : 0.039 0.125 965 Planarity : 0.003 0.024 1165 Dihedral : 4.138 35.994 967 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.73 % Allowed : 17.84 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.31), residues: 788 helix: 1.71 (0.26), residues: 401 sheet: -1.43 (0.67), residues: 60 loop : -0.22 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.006 0.001 HIS A 374 PHE 0.024 0.001 PHE A 315 TYR 0.008 0.001 TYR A 497 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7975 (mmmm) cc_final: 0.7267 (pttt) REVERT: A 474 MET cc_start: 0.7474 (mmp) cc_final: 0.6763 (mmp) REVERT: A 557 MET cc_start: 0.8730 (tmm) cc_final: 0.8483 (tmm) REVERT: C 378 LYS cc_start: 0.6390 (mtpt) cc_final: 0.6133 (ptmm) REVERT: C 409 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7241 (mp10) outliers start: 12 outliers final: 11 residues processed: 106 average time/residue: 0.1829 time to fit residues: 26.1143 Evaluate side-chains 105 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6657 Z= 0.144 Angle : 0.509 9.255 9050 Z= 0.255 Chirality : 0.039 0.127 965 Planarity : 0.003 0.024 1165 Dihedral : 3.956 33.595 965 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 17.84 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.31), residues: 788 helix: 1.76 (0.26), residues: 403 sheet: -1.02 (0.74), residues: 50 loop : -0.24 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.015 0.001 PHE A 315 TYR 0.010 0.001 TYR A 381 ARG 0.002 0.000 ARG A 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7988 (mmmm) cc_final: 0.7266 (pttt) REVERT: A 474 MET cc_start: 0.7498 (mmp) cc_final: 0.6751 (mmp) REVERT: A 476 LYS cc_start: 0.7591 (tppt) cc_final: 0.6986 (mmtp) REVERT: C 409 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7228 (mp10) outliers start: 15 outliers final: 14 residues processed: 103 average time/residue: 0.2017 time to fit residues: 28.1985 Evaluate side-chains 108 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 0.0050 chunk 63 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.0670 chunk 41 optimal weight: 5.9990 overall best weight: 0.5934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.157808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124432 restraints weight = 12670.311| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.45 r_work: 0.3130 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6657 Z= 0.137 Angle : 0.505 9.246 9050 Z= 0.251 Chirality : 0.039 0.133 965 Planarity : 0.003 0.024 1165 Dihedral : 3.769 29.969 965 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.16 % Allowed : 17.70 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.31), residues: 788 helix: 1.87 (0.26), residues: 402 sheet: -0.94 (0.75), residues: 50 loop : -0.21 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.006 0.001 HIS A 374 PHE 0.016 0.001 PHE A 315 TYR 0.009 0.001 TYR A 516 ARG 0.001 0.000 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1795.70 seconds wall clock time: 33 minutes 28.93 seconds (2008.93 seconds total)